Pilsbry (frequently misspelled Pilsbury) spent his childhood and youth in Iowa. He was called "Harry" Pilsbry then, and developed an early fascination with the limited variety of mollusks he was able to find. He attended the University of Iowa, and received the Bachelor of Science degree there in 1882, but did not immediately find employment in his field of interest. Instead, Henry Pilsbry worked for publishing firms and newspapers for the next several years, but devoted most of his spare time to the study of mollusks.
In 1887, he found employment in New York City as a proofreader, but soon met George Washington Tryon, the resident expert on mollusks at the Academy of Natural Sciences of Philadelphia, and architect and author of the ongoing multi-volume Manual of Concology. This meeting led, within a few months, to Tryon's hiring Pilsbry as an assistant. He was, no doubt, impressed by the young man's talents as a proofreader, considerable expertise in technical illustration, and especially by his undeniable enthusiasm for the study of mollusks and substantial knowledge of the subject.
Less than three months after Pilsbry began his new job, George Tryon died and his new assistant, only 25 years old, perhaps to the surprise of some, inherited the titles of "Conservator of the Conchology Section" and "Editor" of the Manual of Conchology.
Pilsbry soon proved capable of prodigious efforts, and his scientific output was remarkable. During the next five years he produced hundreds of detailed pages of the Manual of Conchology, preparing many of the plates himself, and founded The Nautilus, an influential journal of malacology which has survived into the 21st century. He also married during this period, to Adeline Avery. His college, the University of Iowa, honored him with a Doctor of Science degree in 1899 (and he later received two other honorary doctorates: University of Pennsylvania, 1940, and Temple University, 1941). In 1929 he participated in the Pinchot South Sea Expedition. Pilsbry was the first president of the American Malacological Union (Society) founded in 1931.
For almost all of the next 57 years of his long life, Henry Pilsbry spent his hours writing scientific papers, over 3,000 of them, mostly while at the Academy of Natural Sciences. Most of his longest papers were published by the Academy. The shorter ones could usually be found in The Nautilus. The large majority of his work carried only his name, although there were sometimes joint or junior authors, some of whom were more patron than scientist. It is notable that Pilsbry did not always confine himself to the several areas of study with which he was already closely associated, but rather would sometimes stray into other fields of science, from geology and paleontology to the taxonomy of brachiopods.
His field work provided a steady supply of new specimens for study, dissection, and illustration, and a seemingly endless array of new species to name. Pilsbry named 5680 organisms; a full list was published in a 218-page volume. Pilsbry performed extensive amounts of field work, and was clearly an expert in dealing with the outdoors, no matter the conditions. He collected mollusks over virtually the entire United States, and in an atlas of countries: Argentina, Australia, Bahamas, Cocos Islands, Cuba, Galapagos Islands, Guatemala, Marquesas Islands, Mexico, Panama, Peru, and other locations as well. His intellectual reach extended even further, through joint efforts with other workers: especially notably Africa with Joseph Bequaert and the Japanese region with Yoichiro Hirase.
Pilsbry suffered a heart attack in late 1957 while working at the Philadelphia Academy. He seemed to recover from this serious occurrence, but died at his winter home in Florida, about a month and a half later, from a similar event.
Henry Augustus Pilsbry is buried in Bala Cynwyd, Pennsylvania, at St. Asaph's Church.
A species of Cuban dwarf boa, Tropidophis pilsbryi, is named in his honor.